Multiple sequence alignment - TraesCS6B01G188200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G188200 chr6B 100.000 2983 0 0 1 2983 216630752 216633734 0.000000e+00 5509.0
1 TraesCS6B01G188200 chr6B 91.349 578 50 0 1 578 20313848 20313271 0.000000e+00 791.0
2 TraesCS6B01G188200 chr6D 92.007 2152 128 24 836 2958 122989519 122991655 0.000000e+00 2981.0
3 TraesCS6B01G188200 chr6D 94.315 1759 46 26 1 1748 122978698 122980413 0.000000e+00 2645.0
4 TraesCS6B01G188200 chr6D 92.526 1057 44 11 719 1758 124609584 124608546 0.000000e+00 1482.0
5 TraesCS6B01G188200 chr6D 90.510 569 54 0 1 569 10734223 10733655 0.000000e+00 752.0
6 TraesCS6B01G188200 chr6D 90.637 502 19 9 2485 2958 122982029 122982530 2.510000e-180 641.0
7 TraesCS6B01G188200 chr6D 83.131 658 48 32 1863 2492 122980463 122981085 2.620000e-150 542.0
8 TraesCS6B01G188200 chr6D 76.838 544 65 41 1863 2386 124608481 124607979 1.780000e-62 250.0
9 TraesCS6B01G188200 chr6D 82.667 150 26 0 438 587 10731986 10731837 1.870000e-27 134.0
10 TraesCS6B01G188200 chr6A 89.992 2378 132 48 628 2958 158245802 158243484 0.000000e+00 2976.0
11 TraesCS6B01G188200 chr6A 96.645 626 21 0 1 626 158247589 158246964 0.000000e+00 1040.0
12 TraesCS6B01G188200 chr6A 86.247 858 91 11 914 1758 107264411 107265254 0.000000e+00 905.0
13 TraesCS6B01G188200 chr6A 85.929 533 48 13 184 692 12313456 12312927 7.270000e-151 544.0
14 TraesCS6B01G188200 chr6A 89.806 206 6 7 841 1046 158246112 158245922 1.780000e-62 250.0
15 TraesCS6B01G188200 chr6A 90.411 146 14 0 1 146 12313599 12313454 3.030000e-45 193.0
16 TraesCS6B01G188200 chr7D 87.966 1072 61 15 1863 2927 545652595 545653605 0.000000e+00 1203.0
17 TraesCS6B01G188200 chr7D 86.945 1103 78 27 1863 2958 518774808 518775851 0.000000e+00 1179.0
18 TraesCS6B01G188200 chr7D 89.281 737 55 6 992 1713 518768984 518769711 0.000000e+00 902.0
19 TraesCS6B01G188200 chr7D 86.159 867 75 24 919 1758 545647062 545647910 0.000000e+00 894.0
20 TraesCS6B01G188200 chr7D 87.437 788 63 18 983 1758 545650576 545651339 0.000000e+00 874.0
21 TraesCS6B01G188200 chr7D 84.352 671 83 11 1013 1676 530110906 530111561 3.240000e-179 638.0
22 TraesCS6B01G188200 chr7D 80.200 500 53 23 1850 2332 509572864 509572394 1.710000e-87 333.0
23 TraesCS6B01G188200 chr7D 86.149 296 28 7 1797 2085 509597929 509597640 1.040000e-79 307.0
24 TraesCS6B01G188200 chr7D 78.672 497 50 36 1913 2386 545651404 545651867 2.260000e-71 279.0
25 TraesCS6B01G188200 chr7D 84.112 107 2 3 760 866 545646943 545647034 4.100000e-14 89.8
26 TraesCS6B01G188200 chr7D 97.727 44 1 0 2382 2425 545651919 545651962 3.190000e-10 76.8
27 TraesCS6B01G188200 chr7B 88.867 1006 52 18 1863 2855 589937085 589938043 0.000000e+00 1182.0
28 TraesCS6B01G188200 chr7B 85.757 1011 83 23 760 1758 589700825 589699864 0.000000e+00 1013.0
29 TraesCS6B01G188200 chr7B 84.655 769 81 16 983 1740 588823375 588822633 0.000000e+00 732.0
30 TraesCS6B01G188200 chr7B 80.189 424 53 20 1881 2296 537746246 537745846 3.760000e-74 289.0
31 TraesCS6B01G188200 chr7B 78.683 319 54 11 173 481 105520337 105520651 1.810000e-47 200.0
32 TraesCS6B01G188200 chr7B 90.323 124 10 2 2264 2386 589698199 589698077 8.560000e-36 161.0
33 TraesCS6B01G188200 chr7B 97.727 44 1 0 2382 2425 589936404 589936447 3.190000e-10 76.8
34 TraesCS6B01G188200 chr7A 85.727 1100 77 35 1863 2958 594449303 594450326 0.000000e+00 1088.0
35 TraesCS6B01G188200 chr7A 85.531 1016 103 26 1008 2008 626992528 626991542 0.000000e+00 1022.0
36 TraesCS6B01G188200 chr7A 88.902 856 49 12 2122 2958 169955551 169954723 0.000000e+00 1013.0
37 TraesCS6B01G188200 chr7A 87.936 746 68 8 982 1712 594434566 594435304 0.000000e+00 859.0
38 TraesCS6B01G188200 chr7A 84.491 864 100 24 908 1758 627232527 627231685 0.000000e+00 822.0
39 TraesCS6B01G188200 chr7A 81.662 1047 109 40 748 1758 628390147 628389148 0.000000e+00 793.0
40 TraesCS6B01G188200 chr7A 92.837 349 23 2 2580 2927 628647687 628648034 3.430000e-139 505.0
41 TraesCS6B01G188200 chr7A 90.270 185 12 3 2204 2386 628647319 628647499 1.380000e-58 237.0
42 TraesCS6B01G188200 chr7A 94.118 136 4 2 2382 2514 628647536 628647670 1.400000e-48 204.0
43 TraesCS6B01G188200 chr7A 78.261 230 29 11 1935 2155 628485186 628484969 8.680000e-26 128.0
44 TraesCS6B01G188200 chr1B 85.539 1058 79 31 741 1758 398840601 398839578 0.000000e+00 1038.0
45 TraesCS6B01G188200 chr1B 88.054 745 74 2 1008 1740 398962051 398962792 0.000000e+00 869.0
46 TraesCS6B01G188200 chr1B 89.840 187 13 5 2204 2386 398839188 398839004 4.970000e-58 235.0
47 TraesCS6B01G188200 chr1B 82.288 271 34 12 223 480 627944873 627944604 3.870000e-54 222.0
48 TraesCS6B01G188200 chr1B 79.618 157 22 5 2020 2167 398838381 398838226 1.460000e-18 104.0
49 TraesCS6B01G188200 chr5D 85.120 793 90 20 982 1758 289421021 289420241 0.000000e+00 785.0
50 TraesCS6B01G188200 chr5D 80.838 501 59 19 2467 2958 331839058 331839530 2.830000e-95 359.0
51 TraesCS6B01G188200 chr5D 84.085 377 26 21 2458 2823 42080292 42079939 1.710000e-87 333.0
52 TraesCS6B01G188200 chr5D 89.270 233 21 3 1840 2068 30056602 30056834 3.760000e-74 289.0
53 TraesCS6B01G188200 chr3B 80.000 320 44 16 179 482 63462432 63462117 5.010000e-53 219.0
54 TraesCS6B01G188200 chr3B 77.044 318 55 14 175 480 64306808 64306497 1.840000e-37 167.0
55 TraesCS6B01G188200 chr3D 80.323 310 39 18 190 482 40187143 40186839 6.480000e-52 215.0
56 TraesCS6B01G188200 chr3D 81.659 229 19 10 777 986 43727724 43727500 5.110000e-38 169.0
57 TraesCS6B01G188200 chr4A 78.387 310 46 17 193 489 670976386 670976687 6.570000e-42 182.0
58 TraesCS6B01G188200 chr3A 83.085 201 25 7 290 481 51579850 51579650 1.100000e-39 174.0
59 TraesCS6B01G188200 chr3A 85.065 154 15 4 835 986 55501505 55501358 1.850000e-32 150.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G188200 chr6B 216630752 216633734 2982 False 5509.000000 5509 100.000000 1 2983 1 chr6B.!!$F1 2982
1 TraesCS6B01G188200 chr6B 20313271 20313848 577 True 791.000000 791 91.349000 1 578 1 chr6B.!!$R1 577
2 TraesCS6B01G188200 chr6D 122989519 122991655 2136 False 2981.000000 2981 92.007000 836 2958 1 chr6D.!!$F1 2122
3 TraesCS6B01G188200 chr6D 122978698 122982530 3832 False 1276.000000 2645 89.361000 1 2958 3 chr6D.!!$F2 2957
4 TraesCS6B01G188200 chr6D 124607979 124609584 1605 True 866.000000 1482 84.682000 719 2386 2 chr6D.!!$R2 1667
5 TraesCS6B01G188200 chr6D 10731837 10734223 2386 True 443.000000 752 86.588500 1 587 2 chr6D.!!$R1 586
6 TraesCS6B01G188200 chr6A 158243484 158247589 4105 True 1422.000000 2976 92.147667 1 2958 3 chr6A.!!$R2 2957
7 TraesCS6B01G188200 chr6A 107264411 107265254 843 False 905.000000 905 86.247000 914 1758 1 chr6A.!!$F1 844
8 TraesCS6B01G188200 chr6A 12312927 12313599 672 True 368.500000 544 88.170000 1 692 2 chr6A.!!$R1 691
9 TraesCS6B01G188200 chr7D 518774808 518775851 1043 False 1179.000000 1179 86.945000 1863 2958 1 chr7D.!!$F2 1095
10 TraesCS6B01G188200 chr7D 518768984 518769711 727 False 902.000000 902 89.281000 992 1713 1 chr7D.!!$F1 721
11 TraesCS6B01G188200 chr7D 530110906 530111561 655 False 638.000000 638 84.352000 1013 1676 1 chr7D.!!$F3 663
12 TraesCS6B01G188200 chr7D 545646943 545653605 6662 False 569.433333 1203 87.012167 760 2927 6 chr7D.!!$F4 2167
13 TraesCS6B01G188200 chr7B 588822633 588823375 742 True 732.000000 732 84.655000 983 1740 1 chr7B.!!$R2 757
14 TraesCS6B01G188200 chr7B 589936404 589938043 1639 False 629.400000 1182 93.297000 1863 2855 2 chr7B.!!$F2 992
15 TraesCS6B01G188200 chr7B 589698077 589700825 2748 True 587.000000 1013 88.040000 760 2386 2 chr7B.!!$R3 1626
16 TraesCS6B01G188200 chr7A 594449303 594450326 1023 False 1088.000000 1088 85.727000 1863 2958 1 chr7A.!!$F2 1095
17 TraesCS6B01G188200 chr7A 626991542 626992528 986 True 1022.000000 1022 85.531000 1008 2008 1 chr7A.!!$R2 1000
18 TraesCS6B01G188200 chr7A 169954723 169955551 828 True 1013.000000 1013 88.902000 2122 2958 1 chr7A.!!$R1 836
19 TraesCS6B01G188200 chr7A 594434566 594435304 738 False 859.000000 859 87.936000 982 1712 1 chr7A.!!$F1 730
20 TraesCS6B01G188200 chr7A 627231685 627232527 842 True 822.000000 822 84.491000 908 1758 1 chr7A.!!$R3 850
21 TraesCS6B01G188200 chr7A 628389148 628390147 999 True 793.000000 793 81.662000 748 1758 1 chr7A.!!$R4 1010
22 TraesCS6B01G188200 chr7A 628647319 628648034 715 False 315.333333 505 92.408333 2204 2927 3 chr7A.!!$F3 723
23 TraesCS6B01G188200 chr1B 398962051 398962792 741 False 869.000000 869 88.054000 1008 1740 1 chr1B.!!$F1 732
24 TraesCS6B01G188200 chr1B 398838226 398840601 2375 True 459.000000 1038 84.999000 741 2386 3 chr1B.!!$R2 1645
25 TraesCS6B01G188200 chr5D 289420241 289421021 780 True 785.000000 785 85.120000 982 1758 1 chr5D.!!$R2 776

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
903 2576 1.001020 TGATTGCCGCCAGTTCCAT 60.001 52.632 0.0 0.0 0.0 3.41 F
1291 3063 0.109597 CCGCCAACATCAAGCTTCAC 60.110 55.000 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 7019 0.031043 CGGCTCTGCTCTCTCTGATG 59.969 60.0 0.00 0.0 0.0 3.07 R
2963 12185 0.898326 AAAACCGGTGATCTTGCCCC 60.898 55.0 8.52 0.0 0.0 5.80 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
455 456 1.673665 GGAGCACCAGCCACAGAAG 60.674 63.158 0.00 0.00 43.56 2.85
626 1122 3.120199 CGATCGGCCAGCCTATTTATTTG 60.120 47.826 7.38 0.00 0.00 2.32
667 2325 7.396055 GGCAACATATGGTGGTTTATGGTATAT 59.604 37.037 22.01 0.00 32.22 0.86
668 2326 9.456147 GCAACATATGGTGGTTTATGGTATATA 57.544 33.333 22.01 0.00 32.22 0.86
770 2431 1.717194 ACAAGTGTTGTTGTCGTCGT 58.283 45.000 0.00 0.00 42.22 4.34
809 2470 2.993899 ACAAGTTGGAAAGATAGCGTCG 59.006 45.455 7.96 0.00 0.00 5.12
818 2479 4.409570 GAAAGATAGCGTCGTCACAGTAA 58.590 43.478 0.00 0.00 0.00 2.24
901 2574 2.409870 CCTGATTGCCGCCAGTTCC 61.410 63.158 0.00 0.00 0.00 3.62
903 2576 1.001020 TGATTGCCGCCAGTTCCAT 60.001 52.632 0.00 0.00 0.00 3.41
1029 2762 3.362797 TTGCTCTCGCGACTCCGT 61.363 61.111 3.71 0.00 39.65 4.69
1133 2866 4.379243 CCTGCTTCTCCCGCGTGT 62.379 66.667 4.92 0.00 0.00 4.49
1291 3063 0.109597 CCGCCAACATCAAGCTTCAC 60.110 55.000 0.00 0.00 0.00 3.18
1676 6936 1.815421 GCGATGGCTCATCAACGGT 60.815 57.895 13.41 0.00 40.54 4.83
1730 6990 1.093159 GCTCAAGTGATGGAAGCAGG 58.907 55.000 0.00 0.00 24.12 4.85
1750 7010 4.337555 CAGGGGAAGAAATCATAAGCAGTG 59.662 45.833 0.00 0.00 0.00 3.66
1751 7011 3.067320 GGGGAAGAAATCATAAGCAGTGC 59.933 47.826 7.13 7.13 0.00 4.40
1752 7012 3.696051 GGGAAGAAATCATAAGCAGTGCA 59.304 43.478 19.20 0.00 0.00 4.57
1753 7013 4.201990 GGGAAGAAATCATAAGCAGTGCAG 60.202 45.833 19.20 4.19 0.00 4.41
1755 7015 5.448360 GGAAGAAATCATAAGCAGTGCAGTC 60.448 44.000 19.20 2.41 0.00 3.51
1756 7016 4.841422 AGAAATCATAAGCAGTGCAGTCT 58.159 39.130 19.20 4.67 0.00 3.24
1757 7017 5.251764 AGAAATCATAAGCAGTGCAGTCTT 58.748 37.500 19.20 5.16 0.00 3.01
1758 7018 6.409704 AGAAATCATAAGCAGTGCAGTCTTA 58.590 36.000 19.20 7.45 0.00 2.10
1759 7019 6.314896 AGAAATCATAAGCAGTGCAGTCTTAC 59.685 38.462 19.20 1.03 0.00 2.34
1760 7020 4.535526 TCATAAGCAGTGCAGTCTTACA 57.464 40.909 19.20 0.00 0.00 2.41
1762 7022 5.111989 TCATAAGCAGTGCAGTCTTACATC 58.888 41.667 19.20 0.00 0.00 3.06
1763 7023 3.407424 AAGCAGTGCAGTCTTACATCA 57.593 42.857 19.20 0.00 0.00 3.07
1764 7024 2.969990 AGCAGTGCAGTCTTACATCAG 58.030 47.619 19.20 0.00 0.00 2.90
1767 7027 3.367806 GCAGTGCAGTCTTACATCAGAGA 60.368 47.826 11.09 0.00 0.00 3.10
1768 7028 4.422840 CAGTGCAGTCTTACATCAGAGAG 58.577 47.826 0.00 0.00 0.00 3.20
1769 7029 4.157472 CAGTGCAGTCTTACATCAGAGAGA 59.843 45.833 0.00 0.00 0.00 3.10
1770 7030 4.398988 AGTGCAGTCTTACATCAGAGAGAG 59.601 45.833 0.00 0.00 0.00 3.20
1771 7031 3.130164 TGCAGTCTTACATCAGAGAGAGC 59.870 47.826 0.00 0.00 0.00 4.09
1773 7033 4.734402 GCAGTCTTACATCAGAGAGAGCAG 60.734 50.000 0.00 0.00 0.00 4.24
1774 7034 4.639755 CAGTCTTACATCAGAGAGAGCAGA 59.360 45.833 0.00 0.00 0.00 4.26
1775 7035 4.883585 AGTCTTACATCAGAGAGAGCAGAG 59.116 45.833 0.00 0.00 0.00 3.35
1776 7036 3.631686 TCTTACATCAGAGAGAGCAGAGC 59.368 47.826 0.00 0.00 0.00 4.09
1778 7038 0.031043 CATCAGAGAGAGCAGAGCCG 59.969 60.000 0.00 0.00 0.00 5.52
1779 7039 0.106769 ATCAGAGAGAGCAGAGCCGA 60.107 55.000 0.00 0.00 0.00 5.54
1780 7040 1.029408 TCAGAGAGAGCAGAGCCGAC 61.029 60.000 0.00 0.00 0.00 4.79
1781 7041 1.001517 AGAGAGAGCAGAGCCGACA 60.002 57.895 0.00 0.00 0.00 4.35
1782 7042 1.031571 AGAGAGAGCAGAGCCGACAG 61.032 60.000 0.00 0.00 0.00 3.51
1784 7044 1.153862 GAGAGCAGAGCCGACAGTG 60.154 63.158 0.00 0.00 0.00 3.66
1785 7045 1.872197 GAGAGCAGAGCCGACAGTGT 61.872 60.000 0.00 0.00 0.00 3.55
1786 7046 0.609406 AGAGCAGAGCCGACAGTGTA 60.609 55.000 0.00 0.00 0.00 2.90
1787 7047 0.456995 GAGCAGAGCCGACAGTGTAC 60.457 60.000 0.00 0.00 0.00 2.90
1789 7049 0.456995 GCAGAGCCGACAGTGTACTC 60.457 60.000 10.89 10.89 0.00 2.59
1790 7050 1.169577 CAGAGCCGACAGTGTACTCT 58.830 55.000 14.25 14.25 38.22 3.24
1791 7051 1.542030 CAGAGCCGACAGTGTACTCTT 59.458 52.381 16.42 4.37 35.57 2.85
1793 7053 2.748532 AGAGCCGACAGTGTACTCTTAC 59.251 50.000 14.25 0.00 34.06 2.34
1794 7054 1.817447 AGCCGACAGTGTACTCTTACC 59.183 52.381 0.00 0.00 0.00 2.85
1796 7056 3.012518 GCCGACAGTGTACTCTTACCTA 58.987 50.000 0.00 0.00 0.00 3.08
1797 7057 3.065095 GCCGACAGTGTACTCTTACCTAG 59.935 52.174 0.00 0.00 0.00 3.02
1800 7060 5.114780 CGACAGTGTACTCTTACCTAGCTA 58.885 45.833 0.00 0.00 0.00 3.32
1801 7061 5.583854 CGACAGTGTACTCTTACCTAGCTAA 59.416 44.000 0.00 0.00 0.00 3.09
1802 7062 6.238157 CGACAGTGTACTCTTACCTAGCTAAG 60.238 46.154 0.00 0.00 0.00 2.18
1803 7063 6.719301 ACAGTGTACTCTTACCTAGCTAAGA 58.281 40.000 7.21 7.21 32.80 2.10
1804 7064 7.173722 ACAGTGTACTCTTACCTAGCTAAGAA 58.826 38.462 8.52 0.00 33.30 2.52
1807 7067 8.741841 AGTGTACTCTTACCTAGCTAAGAAAAG 58.258 37.037 8.52 0.37 33.30 2.27
1808 7068 7.488792 GTGTACTCTTACCTAGCTAAGAAAAGC 59.511 40.741 8.52 0.00 43.11 3.51
1810 7070 7.005709 ACTCTTACCTAGCTAAGAAAAGCAA 57.994 36.000 8.52 0.00 45.30 3.91
1812 7072 7.604545 ACTCTTACCTAGCTAAGAAAAGCAAAG 59.395 37.037 8.52 0.00 45.30 2.77
1814 7074 4.398319 ACCTAGCTAAGAAAAGCAAAGCA 58.602 39.130 0.00 0.00 45.30 3.91
1815 7075 4.457257 ACCTAGCTAAGAAAAGCAAAGCAG 59.543 41.667 0.00 0.00 45.30 4.24
1816 7076 4.697352 CCTAGCTAAGAAAAGCAAAGCAGA 59.303 41.667 0.00 0.00 45.30 4.26
1817 7077 4.762956 AGCTAAGAAAAGCAAAGCAGAG 57.237 40.909 0.00 0.00 45.30 3.35
1820 7080 3.806625 AAGAAAAGCAAAGCAGAGCAA 57.193 38.095 0.00 0.00 0.00 3.91
1821 7081 3.366440 AGAAAAGCAAAGCAGAGCAAG 57.634 42.857 0.00 0.00 0.00 4.01
1824 7084 3.806625 AAAGCAAAGCAGAGCAAGAAA 57.193 38.095 0.00 0.00 0.00 2.52
1827 7087 2.035576 AGCAAAGCAGAGCAAGAAAAGG 59.964 45.455 0.00 0.00 0.00 3.11
1828 7088 2.035066 GCAAAGCAGAGCAAGAAAAGGA 59.965 45.455 0.00 0.00 0.00 3.36
1830 7090 4.296690 CAAAGCAGAGCAAGAAAAGGAAG 58.703 43.478 0.00 0.00 0.00 3.46
1831 7091 2.512705 AGCAGAGCAAGAAAAGGAAGG 58.487 47.619 0.00 0.00 0.00 3.46
1832 7092 1.543358 GCAGAGCAAGAAAAGGAAGGG 59.457 52.381 0.00 0.00 0.00 3.95
1833 7093 2.815589 GCAGAGCAAGAAAAGGAAGGGA 60.816 50.000 0.00 0.00 0.00 4.20
1834 7094 3.694926 CAGAGCAAGAAAAGGAAGGGAT 58.305 45.455 0.00 0.00 0.00 3.85
1837 7097 4.289672 AGAGCAAGAAAAGGAAGGGATACA 59.710 41.667 0.00 0.00 39.74 2.29
1838 7098 4.593956 AGCAAGAAAAGGAAGGGATACAG 58.406 43.478 0.00 0.00 39.74 2.74
1839 7099 4.043435 AGCAAGAAAAGGAAGGGATACAGT 59.957 41.667 0.00 0.00 39.74 3.55
1840 7100 4.767409 GCAAGAAAAGGAAGGGATACAGTT 59.233 41.667 0.00 0.00 39.74 3.16
1841 7101 5.335976 GCAAGAAAAGGAAGGGATACAGTTG 60.336 44.000 0.00 0.00 39.74 3.16
1842 7102 5.584551 AGAAAAGGAAGGGATACAGTTGT 57.415 39.130 0.00 0.00 39.74 3.32
1843 7103 5.561679 AGAAAAGGAAGGGATACAGTTGTC 58.438 41.667 0.00 0.00 39.74 3.18
1844 7104 4.993705 AAAGGAAGGGATACAGTTGTCA 57.006 40.909 0.00 0.00 39.74 3.58
1846 7106 4.287766 AGGAAGGGATACAGTTGTCAAC 57.712 45.455 7.68 7.68 39.74 3.18
1850 7110 5.817816 GGAAGGGATACAGTTGTCAACTATG 59.182 44.000 17.76 10.26 40.46 2.23
1852 7112 7.364408 GGAAGGGATACAGTTGTCAACTATGTA 60.364 40.741 17.76 16.74 40.46 2.29
1853 7113 7.490657 AGGGATACAGTTGTCAACTATGTAA 57.509 36.000 17.76 3.04 40.46 2.41
1854 7114 8.090788 AGGGATACAGTTGTCAACTATGTAAT 57.909 34.615 17.76 7.36 40.46 1.89
1855 7115 8.204836 AGGGATACAGTTGTCAACTATGTAATC 58.795 37.037 17.76 14.25 40.46 1.75
1856 7116 8.204836 GGGATACAGTTGTCAACTATGTAATCT 58.795 37.037 17.76 4.14 40.46 2.40
1879 8685 4.003648 ACTAATTGCAAGTGTGTAGGAGC 58.996 43.478 10.14 0.00 0.00 4.70
1992 8813 5.355596 TGCAAGGGTTTTGTTTCATGTAAG 58.644 37.500 0.00 0.00 0.00 2.34
1999 8820 7.232534 AGGGTTTTGTTTCATGTAAGAGCATTA 59.767 33.333 0.00 0.00 0.00 1.90
2012 8833 8.697507 TGTAAGAGCATTAGATCTGATCAGTA 57.302 34.615 21.92 9.67 40.18 2.74
2039 8865 2.159071 TATGCAAACATCTGCCATTGGC 60.159 45.455 21.12 21.12 42.63 4.52
2193 9072 3.565902 CAGATATGTGTGCTCTACTCCGA 59.434 47.826 0.00 0.00 0.00 4.55
2332 10436 5.356751 TGTGTACTTGCTGTCTGAATTTTGT 59.643 36.000 0.00 0.00 0.00 2.83
2419 10586 2.646930 TCATTGACATGGATCCACTGC 58.353 47.619 18.99 9.59 0.00 4.40
2446 10616 3.944650 ACATATTCAGTACAATTGCCGCA 59.055 39.130 5.05 0.00 0.00 5.69
2526 11648 4.160252 GGTGCCAGTATCAAATCAAACCAT 59.840 41.667 0.00 0.00 0.00 3.55
2529 11651 7.417797 GGTGCCAGTATCAAATCAAACCATATT 60.418 37.037 0.00 0.00 0.00 1.28
2549 11673 2.148916 TCACGTCGCAGAGAAAATGT 57.851 45.000 0.00 0.00 36.95 2.71
2756 11909 3.144506 CTCTGCACCTTCAAGTGTCATT 58.855 45.455 0.00 0.00 40.04 2.57
2935 12157 5.946942 TGGGCTTTATCCATTGCATTTTA 57.053 34.783 0.00 0.00 0.00 1.52
2960 12182 6.721208 ACCATGATCAATACTTCAAAACTGGT 59.279 34.615 0.00 0.80 30.43 4.00
2961 12183 7.233348 ACCATGATCAATACTTCAAAACTGGTT 59.767 33.333 0.00 0.00 30.91 3.67
2963 12185 8.918658 CATGATCAATACTTCAAAACTGGTTTG 58.081 33.333 11.89 11.89 46.86 2.93
2964 12186 7.432869 TGATCAATACTTCAAAACTGGTTTGG 58.567 34.615 17.41 5.70 45.73 3.28
2965 12187 6.155475 TCAATACTTCAAAACTGGTTTGGG 57.845 37.500 17.41 12.81 45.73 4.12
2966 12188 5.069781 TCAATACTTCAAAACTGGTTTGGGG 59.930 40.000 17.41 12.50 45.73 4.96
2967 12189 1.484653 ACTTCAAAACTGGTTTGGGGC 59.515 47.619 17.41 0.00 45.73 5.80
2968 12190 1.484240 CTTCAAAACTGGTTTGGGGCA 59.516 47.619 17.41 0.00 45.73 5.36
2969 12191 1.573108 TCAAAACTGGTTTGGGGCAA 58.427 45.000 17.41 0.00 45.73 4.52
2970 12192 1.484240 TCAAAACTGGTTTGGGGCAAG 59.516 47.619 17.41 0.00 45.73 4.01
2971 12193 1.484240 CAAAACTGGTTTGGGGCAAGA 59.516 47.619 10.30 0.00 42.57 3.02
2973 12195 1.632589 AACTGGTTTGGGGCAAGATC 58.367 50.000 0.00 0.00 0.00 2.75
2974 12196 0.482446 ACTGGTTTGGGGCAAGATCA 59.518 50.000 0.00 0.00 0.00 2.92
2975 12197 0.890683 CTGGTTTGGGGCAAGATCAC 59.109 55.000 0.00 0.00 0.00 3.06
2977 12199 1.595093 GGTTTGGGGCAAGATCACCG 61.595 60.000 0.00 0.00 0.00 4.94
2978 12200 1.304052 TTTGGGGCAAGATCACCGG 60.304 57.895 0.00 0.00 0.00 5.28
2979 12201 2.075355 TTTGGGGCAAGATCACCGGT 62.075 55.000 0.00 0.00 0.00 5.28
2982 12204 0.898326 GGGGCAAGATCACCGGTTTT 60.898 55.000 2.97 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
626 1122 3.161866 TGTTGCCAAAAGAATAGGGTCC 58.838 45.455 0.00 0.00 0.00 4.46
809 2470 8.021396 GGATTTGGACATTTACTTTACTGTGAC 58.979 37.037 0.00 0.00 0.00 3.67
818 2479 2.758423 GCGGGGATTTGGACATTTACTT 59.242 45.455 0.00 0.00 0.00 2.24
901 2574 4.899239 GGAGACGGGGCAGCGATG 62.899 72.222 0.00 0.00 0.00 3.84
1676 6936 5.064707 GGATTTACATCGCTTGAGCAAAGTA 59.935 40.000 3.65 0.00 42.21 2.24
1730 6990 3.696051 TGCACTGCTTATGATTTCTTCCC 59.304 43.478 1.98 0.00 0.00 3.97
1750 7010 3.130164 TGCTCTCTCTGATGTAAGACTGC 59.870 47.826 0.00 0.00 0.00 4.40
1751 7011 4.639755 TCTGCTCTCTCTGATGTAAGACTG 59.360 45.833 0.00 0.00 0.00 3.51
1752 7012 4.854173 TCTGCTCTCTCTGATGTAAGACT 58.146 43.478 0.00 0.00 0.00 3.24
1753 7013 4.498009 GCTCTGCTCTCTCTGATGTAAGAC 60.498 50.000 0.00 0.00 0.00 3.01
1755 7015 3.243501 GGCTCTGCTCTCTCTGATGTAAG 60.244 52.174 0.00 0.00 0.00 2.34
1756 7016 2.692557 GGCTCTGCTCTCTCTGATGTAA 59.307 50.000 0.00 0.00 0.00 2.41
1757 7017 2.305928 GGCTCTGCTCTCTCTGATGTA 58.694 52.381 0.00 0.00 0.00 2.29
1758 7018 1.113788 GGCTCTGCTCTCTCTGATGT 58.886 55.000 0.00 0.00 0.00 3.06
1759 7019 0.031043 CGGCTCTGCTCTCTCTGATG 59.969 60.000 0.00 0.00 0.00 3.07
1760 7020 0.106769 TCGGCTCTGCTCTCTCTGAT 60.107 55.000 0.00 0.00 0.00 2.90
1762 7022 1.311651 TGTCGGCTCTGCTCTCTCTG 61.312 60.000 0.00 0.00 0.00 3.35
1763 7023 1.001517 TGTCGGCTCTGCTCTCTCT 60.002 57.895 0.00 0.00 0.00 3.10
1764 7024 1.312371 ACTGTCGGCTCTGCTCTCTC 61.312 60.000 0.00 0.00 0.00 3.20
1767 7027 0.609406 TACACTGTCGGCTCTGCTCT 60.609 55.000 0.00 0.00 0.00 4.09
1768 7028 0.456995 GTACACTGTCGGCTCTGCTC 60.457 60.000 0.00 0.00 0.00 4.26
1769 7029 0.896019 AGTACACTGTCGGCTCTGCT 60.896 55.000 0.00 0.00 0.00 4.24
1770 7030 0.456995 GAGTACACTGTCGGCTCTGC 60.457 60.000 0.00 0.00 0.00 4.26
1771 7031 1.169577 AGAGTACACTGTCGGCTCTG 58.830 55.000 0.00 0.00 35.48 3.35
1773 7033 2.159407 GGTAAGAGTACACTGTCGGCTC 60.159 54.545 0.00 0.00 31.21 4.70
1774 7034 1.817447 GGTAAGAGTACACTGTCGGCT 59.183 52.381 0.00 0.00 31.21 5.52
1775 7035 1.817447 AGGTAAGAGTACACTGTCGGC 59.183 52.381 0.00 0.00 31.21 5.54
1776 7036 3.065095 GCTAGGTAAGAGTACACTGTCGG 59.935 52.174 0.00 0.00 31.21 4.79
1778 7038 6.822676 TCTTAGCTAGGTAAGAGTACACTGTC 59.177 42.308 31.16 0.00 34.69 3.51
1779 7039 6.719301 TCTTAGCTAGGTAAGAGTACACTGT 58.281 40.000 31.16 0.00 34.69 3.55
1780 7040 7.627298 TTCTTAGCTAGGTAAGAGTACACTG 57.373 40.000 32.08 12.82 39.61 3.66
1781 7041 8.647256 TTTTCTTAGCTAGGTAAGAGTACACT 57.353 34.615 32.08 4.33 39.61 3.55
1782 7042 7.488792 GCTTTTCTTAGCTAGGTAAGAGTACAC 59.511 40.741 32.08 22.03 39.61 2.90
1784 7044 7.545489 TGCTTTTCTTAGCTAGGTAAGAGTAC 58.455 38.462 32.08 24.87 39.61 2.73
1785 7045 7.713734 TGCTTTTCTTAGCTAGGTAAGAGTA 57.286 36.000 32.08 24.54 39.61 2.59
1786 7046 6.607004 TGCTTTTCTTAGCTAGGTAAGAGT 57.393 37.500 32.08 0.00 39.61 3.24
1787 7047 7.413548 GCTTTGCTTTTCTTAGCTAGGTAAGAG 60.414 40.741 32.08 24.97 39.61 2.85
1789 7049 6.149474 TGCTTTGCTTTTCTTAGCTAGGTAAG 59.851 38.462 28.23 28.23 41.76 2.34
1790 7050 6.001460 TGCTTTGCTTTTCTTAGCTAGGTAA 58.999 36.000 13.49 13.49 41.76 2.85
1791 7051 5.556915 TGCTTTGCTTTTCTTAGCTAGGTA 58.443 37.500 2.43 0.00 41.76 3.08
1793 7053 4.697352 TCTGCTTTGCTTTTCTTAGCTAGG 59.303 41.667 0.00 0.00 41.76 3.02
1794 7054 5.673318 GCTCTGCTTTGCTTTTCTTAGCTAG 60.673 44.000 0.00 0.00 41.76 3.42
1796 7056 3.057666 GCTCTGCTTTGCTTTTCTTAGCT 60.058 43.478 0.00 0.00 41.76 3.32
1797 7057 3.240884 GCTCTGCTTTGCTTTTCTTAGC 58.759 45.455 0.00 0.00 41.59 3.09
1800 7060 3.382546 TCTTGCTCTGCTTTGCTTTTCTT 59.617 39.130 0.00 0.00 0.00 2.52
1801 7061 2.954318 TCTTGCTCTGCTTTGCTTTTCT 59.046 40.909 0.00 0.00 0.00 2.52
1802 7062 3.360249 TCTTGCTCTGCTTTGCTTTTC 57.640 42.857 0.00 0.00 0.00 2.29
1803 7063 3.806625 TTCTTGCTCTGCTTTGCTTTT 57.193 38.095 0.00 0.00 0.00 2.27
1804 7064 3.806625 TTTCTTGCTCTGCTTTGCTTT 57.193 38.095 0.00 0.00 0.00 3.51
1807 7067 2.035066 TCCTTTTCTTGCTCTGCTTTGC 59.965 45.455 0.00 0.00 0.00 3.68
1808 7068 3.996150 TCCTTTTCTTGCTCTGCTTTG 57.004 42.857 0.00 0.00 0.00 2.77
1810 7070 2.889678 CCTTCCTTTTCTTGCTCTGCTT 59.110 45.455 0.00 0.00 0.00 3.91
1812 7072 1.543358 CCCTTCCTTTTCTTGCTCTGC 59.457 52.381 0.00 0.00 0.00 4.26
1814 7074 4.289672 TGTATCCCTTCCTTTTCTTGCTCT 59.710 41.667 0.00 0.00 0.00 4.09
1815 7075 4.589908 TGTATCCCTTCCTTTTCTTGCTC 58.410 43.478 0.00 0.00 0.00 4.26
1816 7076 4.043435 ACTGTATCCCTTCCTTTTCTTGCT 59.957 41.667 0.00 0.00 0.00 3.91
1817 7077 4.336280 ACTGTATCCCTTCCTTTTCTTGC 58.664 43.478 0.00 0.00 0.00 4.01
1820 7080 5.073144 TGACAACTGTATCCCTTCCTTTTCT 59.927 40.000 0.00 0.00 0.00 2.52
1821 7081 5.313712 TGACAACTGTATCCCTTCCTTTTC 58.686 41.667 0.00 0.00 0.00 2.29
1824 7084 4.351111 AGTTGACAACTGTATCCCTTCCTT 59.649 41.667 19.96 0.00 41.01 3.36
1827 7087 6.407202 ACATAGTTGACAACTGTATCCCTTC 58.593 40.000 27.44 0.00 42.84 3.46
1828 7088 6.374417 ACATAGTTGACAACTGTATCCCTT 57.626 37.500 27.44 3.90 42.84 3.95
1830 7090 8.204836 AGATTACATAGTTGACAACTGTATCCC 58.795 37.037 27.44 14.68 42.84 3.85
1850 7110 8.818057 CCTACACACTTGCAATTAGTAGATTAC 58.182 37.037 20.64 0.00 31.56 1.89
1852 7112 7.620880 TCCTACACACTTGCAATTAGTAGATT 58.379 34.615 20.64 0.17 31.56 2.40
1853 7113 7.182817 TCCTACACACTTGCAATTAGTAGAT 57.817 36.000 20.64 6.23 31.56 1.98
1854 7114 6.599356 TCCTACACACTTGCAATTAGTAGA 57.401 37.500 20.64 10.53 31.56 2.59
1855 7115 5.292101 GCTCCTACACACTTGCAATTAGTAG 59.708 44.000 15.73 15.73 0.00 2.57
1856 7116 5.175859 GCTCCTACACACTTGCAATTAGTA 58.824 41.667 0.00 0.58 0.00 1.82
1857 7117 4.003648 GCTCCTACACACTTGCAATTAGT 58.996 43.478 0.00 0.00 0.00 2.24
1859 7119 4.014569 TGCTCCTACACACTTGCAATTA 57.985 40.909 0.00 0.00 0.00 1.40
1861 7121 2.566833 TGCTCCTACACACTTGCAAT 57.433 45.000 0.00 0.00 0.00 3.56
1879 8685 3.991773 CTGGAAAACATGCCAGTGAAATG 59.008 43.478 8.51 0.00 45.21 2.32
1956 8765 7.388500 ACAAAACCCTTGCATTAATTGATCAAG 59.612 33.333 14.54 0.71 35.26 3.02
2012 8833 6.659745 ATGGCAGATGTTTGCATACATTAT 57.340 33.333 21.45 12.20 45.86 1.28
2014 8835 5.113383 CAATGGCAGATGTTTGCATACATT 58.887 37.500 21.45 10.52 45.86 2.71
2039 8865 9.381033 ACATCAGATGAAAACATAGAAAGAGAG 57.619 33.333 17.81 0.00 0.00 3.20
2105 8950 8.122472 AGAAATATTCTTGGTGGAATCGTTTT 57.878 30.769 0.00 0.00 36.36 2.43
2146 9006 5.333581 TCCTCTCCTGAAATTCAGTCACTA 58.666 41.667 20.18 2.30 42.80 2.74
2193 9072 6.687081 TGTTGAGGTGTAAATTTTTCTCGT 57.313 33.333 0.00 0.00 0.00 4.18
2261 9141 4.711399 TGTATGCATCAGGATTCAGGAAG 58.289 43.478 0.19 0.00 0.00 3.46
2332 10436 4.046938 TGAACAAAATTTGCAGCCGTTA 57.953 36.364 5.52 0.00 0.00 3.18
2419 10586 6.627276 CGGCAATTGTACTGAATATGTTAACG 59.373 38.462 7.40 0.00 0.00 3.18
2446 10616 2.949177 TGGCAGGTACACATGAGTTT 57.051 45.000 0.00 0.00 0.00 2.66
2526 11648 4.688879 ACATTTTCTCTGCGACGTGAAATA 59.311 37.500 0.00 0.00 0.00 1.40
2529 11651 2.479837 ACATTTTCTCTGCGACGTGAA 58.520 42.857 0.00 0.00 0.00 3.18
2549 11673 7.380536 AGTAAACACCATTGTCGTCAAGTATA 58.619 34.615 0.97 0.00 36.97 1.47
2756 11909 4.135153 GGAGCCGAGAAGCTGCGA 62.135 66.667 5.57 0.00 45.15 5.10
2916 12138 6.985645 TCATGGTAAAATGCAATGGATAAAGC 59.014 34.615 0.00 0.00 0.00 3.51
2917 12139 9.199982 GATCATGGTAAAATGCAATGGATAAAG 57.800 33.333 0.00 0.00 0.00 1.85
2935 12157 6.721208 ACCAGTTTTGAAGTATTGATCATGGT 59.279 34.615 0.00 0.00 32.88 3.55
2958 12180 1.595093 CGGTGATCTTGCCCCAAACC 61.595 60.000 0.00 0.00 0.00 3.27
2960 12182 1.304052 CCGGTGATCTTGCCCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
2961 12183 2.075355 AACCGGTGATCTTGCCCCAA 62.075 55.000 8.52 0.00 0.00 4.12
2963 12185 0.898326 AAAACCGGTGATCTTGCCCC 60.898 55.000 8.52 0.00 0.00 5.80
2964 12186 2.653557 AAAACCGGTGATCTTGCCC 58.346 52.632 8.52 0.00 0.00 5.36


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.